From: I. Camps (
Date: Fri Dec 30 2022 - 14:43:28 CST

Thank you all for your suggestions.

As I just wanted to center all the molecules, the approach proposed by
Giacomo worked like a charm:
- select each molecule in one set
- align/center each set with: $sel moveby [vecscale -1.0 [measure center
- Display --> Reset View



On Thu, Dec 29, 2022 at 5:25 PM Giacomo Fiorin <>

> Hi Camps, can you define a sub-set of atoms (at least three) that the
> molecules have in common and use that as the selection? If they don't
> really have a common structure, you are probably out of luck for aligning
> them rotationally, but at least you can center them all on the origin by
> selecting them one at a time and do the following:
> $sel moveby [vecscale -1.0 [measure center $sel]]
> On Thu, Dec 29, 2022 at 3:06 PM I. Camps <> wrote:
>> Hello,
>> I loaded 5 molecules in VMD. They have different sizes/number of atoms
>> and their origins are in different positions.
>> Now, I want to center (superimpose) all the molecules.
>> Using *align* or *measure fit* is not possible because the number of
>> atoms is different between them.
>> Any help is welcome.
>> Regards,
>> Camps